Metagenomic Data Analysis

ISBN-13: 9781071630716 / Angielski

Suparna Mitra

Opis

This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis using most used R packages. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field. 

Spis treści

1. From genomics to metagenomics in the era of recent sequencing technologies

Saskia Benz and Suparna Mitra

 

2. Quality Control in Metagenomics Data

Abraham Gihawi, Ryan Cardenas, Rachel Hurst, and Daniel S. Brewer

 

3. Metagenomics Databases for Bacteria

Dapeng Wang

 

4. Amplicon Sequencing Pipelines in Metagenomics

Dapeng Wang

 

5. A practical guide to 16S rRNA microbiome analysis in musculoskeletal disorders

Rooney CM and Mitra S^.

 

6. DIAMOND+MEGAN microbiome analysis Anupam Gautam, Wenhuan Zeng, and Daniel H. Huson

 

7. Interactive Web-based Services for Metagenomic Data Analysis and Comparisons

Nehal Adel Abdelsalam, Hajar El-Shora, and Mohamed El-Hadidi

 

8. Application of High Throughput Sequencing (HTS) to Enhance the Well-being of an Endangered Species (Malayan tapir): Characterization of Gut Microbiome using MG-RAST

Ramitha Arumugam,Prithivan Ravichandran, Swee Keong Yeap, Reuben Sunil Kumar Sharma, Shahrizim Bin Zulkifly, Donny Yawah,  and Geetha Annavi

 

9. Designing knowledge-based bioremediation strategies using metagenomics

Niti B. Jadeja and Atya Kapley

 

10. Nanopore sequencing techniques – A comparison of the MinKNOW and the Alignator sequencers

Sebastian Oeck, Alicia I Tüns, an Alexander Schramm

 

^11. MAIRA: protein-based analysis of MinION reads on a laptop

Caner Bağc , Benjamin Albrecht, and Daniel H. Huson

 

12. Recovery and analysis of long read metagenome-assembled genomes

Krithika Arumugam, Irina Bessarab, Mindia A. S. Haryono, and Rohan B.H. Williams

  13. Cloud Computing for Metagenomics: Building a personalised computational platform for pipeline analyses

Martin Callaghan

 

14. Artificial Intelligence in Medicine: Microbiome-based Machine Learning for Phenotypic Classification

Xi Cheng and Bina Joe

 

15. Tracking Antibiotic Resistance From the Environment to Human Health

Eman Abdelrazik and Mohamed El-Hadidi

 

16. Targeted enrichment of low-abundance and uncharacterised taxon members in complex microbial community with primer-free FISH probes

Pui Yi Maria Yung, Shi Ming Tan

 

17. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data

Mihnea R. Mangalea, Kristopher Keift, Breck A. Duerkop, and Karthik Anantharaman

 

18. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data

Mihnea R. Mangalea, Kristopher Keift, Breck A. Duerkop, and Karthik Anantharaman

 

19. Metagenomics Data Visualisation using R

Alex Coleman, Anupam Bose, and Suparna Mitra

 

20. Comprehensive guideline for microbiome analysis using R packages

Joseph N Boctor, Mariam Oweda, and  Mohamed El-Hadidi